Microscopic techniques have been developed to incorporate time-correlated single photon counting. Significant modifications to the confocal apparatus allow for simultaneous two color monitoring of fluorescent tags as well as polarization modulation of probe beams. In addition, numerous mathematical algorithms are being incorporated into the data analysis and further explored to aid in the interpretation of the single molecule emissions, their time correlations and the relationship of them to conformational changes in these assemblies. Investigations into ribosomal translation, GCN-4 peptide conformational dynamics as well as conformational dynamics in light harvesting assemblies are being undertaken (see Highlights).